Variant report

Variant	rs316405
Chromosome Location	chr5:43070866-43070867
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:43064995..43071284-chr5:43119667..43123996,15	MCF-7	breast:
2	chr5:43041801..43042395-chr5:43070350..43070882,2	MCF-7	breast:
3	chr5:43070103..43072247-chr5:43117148..43119199,2	K562	blood:
4	chr5:43070295..43071835-chr5:43373758..43376387,2	MCF-7	breast:
5	chr5:43034726..43053192-chr5:43061725..43074206,66	K562	blood:

Variant related genes	Relation type
ENSG00000172262	Chromatin interaction
ENSG00000215068	Chromatin interaction
ENSG00000177721	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10058374	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs10074873	0.94[JPT][hapmap]
rs10075647	0.80[CHB][hapmap];0.88[JPT][hapmap]
rs10078527	0.88[JPT][hapmap]
rs1032434	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10454865	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10805667	0.93[JPT][hapmap]
rs10941597	0.81[GIH][hapmap]
rs10941607	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10941608	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11550285	0.92[ASN][1000 genomes]
rs11550286	0.93[ASN][1000 genomes]
rs11550287	0.90[CHB][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[ASN][1000 genomes]
rs11740797	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.98[ASN][1000 genomes]
rs11742691	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11743246	0.80[ASN][1000 genomes]
rs11748187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11750239	0.81[ASN][1000 genomes]
rs11949817	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11954543	0.80[ASN][1000 genomes]
rs11956243	0.93[ASN][1000 genomes]
rs12109075	0.80[CHB][hapmap]
rs12188691	0.85[CEU][hapmap];0.89[CHB][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.82[ASN][1000 genomes]
rs13155513	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13159703	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13165504	0.82[ASN][1000 genomes]
rs13169563	0.98[ASN][1000 genomes]
rs13173064	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.93[JPT][hapmap];0.90[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.95[ASN][1000 genomes]
rs13665	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs1532331	0.80[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap]
rs17301375	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2452831	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316398	0.82[CHB][hapmap];0.90[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs316409	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316410	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs316411	0.83[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.82[YRI][hapmap];0.91[ASN][1000 genomes]
rs316418	0.88[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3207358	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34087147	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs34315422	0.95[ASN][1000 genomes]
rs34492794	0.80[ASN][1000 genomes]
rs34670023	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34808919	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34859360	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35085573	0.98[ASN][1000 genomes]
rs35541316	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35953019	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs36039989	0.93[ASN][1000 genomes]
rs36083302	0.95[ASN][1000 genomes]
rs3733839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797312	0.80[ASN][1000 genomes]
rs3849698	0.90[CHB][hapmap];0.85[GIH][hapmap];0.93[JPT][hapmap];0.80[TSI][hapmap];0.80[ASN][1000 genomes]
rs3849699	0.85[CEU][hapmap];0.90[CHB][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.82[ASN][1000 genomes]
rs4498259	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs493097	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504404	0.88[ASN][1000 genomes]
rs514567	0.95[LWK][hapmap]
rs541143	0.93[JPT][hapmap]
rs55939188	0.80[AMR][1000 genomes]
rs56169202	0.82[ASN][1000 genomes]
rs581914	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62367685	0.95[ASN][1000 genomes]
rs62367688	0.96[ASN][1000 genomes]
rs62372869	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6414900	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs6451674	0.80[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap]
rs6451675	0.80[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap]
rs670206	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6862639	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs6864223	0.93[ASN][1000 genomes]
rs6871636	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs6884303	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs6894506	0.82[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap]
rs7701510	0.82[CHB][hapmap]
rs7709181	1.00[ASW][hapmap];0.92[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.96[ASN][1000 genomes]
rs7729529	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7730004	0.80[CHB][hapmap];0.94[JPT][hapmap]
rs9790935	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
7	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
8	nsv870299	chr5:43053679-43107880	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs316405	ZNF131	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43067800-43071200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:43068000-43077600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:43068200-43074200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:43068600-43071200	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr5:43068600-43071200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:43068600-43082600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr5:43068800-43071000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr5:43068800-43071000	Weak transcription	Aorta	Aorta
9	chr5:43069000-43071000	Weak transcription	Gastric	stomach
10	chr5:43069000-43081400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr5:43069200-43071800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr5:43069200-43071800	Genic enhancers	Primary T cells fromperipheralblood	blood
13	chr5:43069200-43074200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr5:43069400-43071000	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr5:43069400-43071000	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr5:43069400-43071000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr5:43069400-43071200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr5:43069400-43071200	Weak transcription	Fetal Brain Female	brain
19	chr5:43069400-43072200	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr5:43069400-43075800	Strong transcription	Fetal Stomach	stomach
21	chr5:43069400-43082800	Weak transcription	Colonic Mucosa	Colon
22	chr5:43069400-43087400	Weak transcription	Stomach Mucosa	stomach
23	chr5:43069600-43071000	Weak transcription	Fetal Lung	lung
24	chr5:43069600-43071000	Weak transcription	Lung	lung
25	chr5:43069600-43071000	Weak transcription	Spleen	Spleen
26	chr5:43069600-43071200	Weak transcription	Pancreas	Pancrea
27	chr5:43069600-43071200	Weak transcription	Right Atrium	heart
28	chr5:43069600-43071200	Weak transcription	NHEK	skin
29	chr5:43069600-43072400	Strong transcription	Primary T cells from cord blood	blood
30	chr5:43069600-43073200	Strong transcription	Placenta	Placenta
31	chr5:43069600-43073400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr5:43069600-43075200	Weak transcription	Fetal Heart	heart
33	chr5:43069600-43077000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:43069600-43080400	Strong transcription	Fetal Muscle Trunk	muscle
35	chr5:43069600-43080400	Strong transcription	Fetal Muscle Leg	muscle
36	chr5:43069800-43071000	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:43069800-43071000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr5:43069800-43071000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr5:43069800-43071800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr5:43069800-43072000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr5:43069800-43076000	Weak transcription	GM12878-XiMat	blood
42	chr5:43070000-43071000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr5:43070000-43071000	Strong transcription	Fetal Thymus	thymus
44	chr5:43070000-43071800	Strong transcription	HUES64 Cell Line	embryonic stem cell
45	chr5:43070000-43071800	Strong transcription	NHLF	lung
46	chr5:43070000-43072200	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr5:43070000-43073400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr5:43070000-43105400	Weak transcription	HSMMtube	muscle
49	chr5:43070200-43071000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr5:43070200-43071000	Weak transcription	Psoas Muscle	Psoas

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